This mission is kind of notoriously buggy, especially in terms of what ship you start out in; I think it's affected by what you flew in the previous mission, even though it shouldn't be. There's no real way to save all eight of the escape pods without flat-out cheating; unfortunately, you can't advance in campaigns in FS1 while cheating, though you could if you were playing Silent Threat through the FS Port in FS2. Although the debriefing does reprimand you, you can advance so long as even one of the pods survives, so try your best to pick off the enemy fighters before they manage to take out all of them, and you should be able to make it through.
And as Kolgena said, if you have FS2, I would highly recommend playing Silent Threat: Reborn. The team basically took the general story of the rather flawed original Silent Threat campaign, greatly expanded on it, added several more missions, and basically made everything make sense. It's a far better experience than the original campaign ever was.